Of Bacteria, Batman, and Yosemite Sam

ORIGINAL: OxBridgeBiotech

By Robert Cooper
Monday, 24th June 2013

In the past few centuries, our understanding of bacteria has progressed from mysterious medieval vapours, to the microscopic “animalcules” of van Leeuwenhoek, to the germ theory of disease à la Pasteur, to the realizations that bacteria outnumber us within our own bodies and that good ”probiotic” bacteria actually make us healthier. Now, a new study seems to have discovered a Batman bacterium. Well, technically, the bacterium was already well-known; the discovery was to show that this prokaryotic Bruce Wayne is, in fact, Batman.

An electron micrograph of Pseudomonas aeruginosa in its
natural environment.

What are the three defining characteristics of Batman?

• First, you don’t want to mess with Batman, for he will mess you up. 
• Second, Batman is a benevolent guardian. Behave yourself, and all will be fine. 
• Third, Batman is multidimensional. He is dark, his morality complex. 

Given those defining characteristics, I submit to you, courtesy of Basler et al. [1], that the bacterial species Pseudomonas aeruginosa is, indeed, Batman.

The bacterial world is a tough one, pockmarked by chemical and biological warfare. (Anthrax, after all, is a completely natural bacterium). In this microscopic world, one of the most common weapons is the type VI secretion system (T6SS), which blasts through opponent bacterial cell walls and delivers (all-natural) biological weapon warheads. P. aeruginosa, our Batman, has stockpiles of T6SS missiles, and it also has a missile defense system to deflect the T6SS of aggressors. UN inspectors are still trying to determine how exactly this defense system works, but Basler et al. suggest it may involve super-strong cell wall armor, a kind of bullet-proof vest, in addition to antidotes for any poison that does get in. Mix P. aeruginosa with other T6SS-packing bacteria, such as Vibrio cholera or Acinetobacter baylyi, and P. aeruginosa wins, pilli down. So Batman feature one – badassness: check.

However, if you mix P. aeruginosa with well-behaving bacteria that are not firing off T6SS’s, it turns out that P. aeruginosa keeps its own T6SS holstered. Even if you disarm the normally aggressive V. cholera by mutating its T6SS genes, P. aeurginosa now leaves it well-enough alone. P. aeruginosa will mess you up, but only if you shoot first. Contrast that with V. cholera, the Yosemite Sam of the bacterial world, which shoots off its T6SS at random but without P. aeruginosa‘s deadly precision. Batman feature two – benevolence: check.


Vibrio cholera has a bit of trouble controlling its T6SS.

As for the third feature of Batman – moral ambiguity – well, remember that P. aeruginosa is known to attack humans as well, especially those with cystic fibrosis. We should also note that P. aeruginosa can be rather high-strung; every once in a while one P. aeruginosa will flash its T6SS (presumably by accident [2], but we can’t discount the possibility that it’s showing off), which can spark violent duels with its neighboring sister cells. Batman feature three: check.

So what exactly is going on here? What role does this bacterial Batman play in microbial Gotham? The study authors suggest that P. aeruginosa may play a kind of sheepdog role, protecting other bacteria within the same biofilm from aggressors. In return, the other bacteria may help break down food that P. aeruginosa couldn’t eat on its own. However, microbial ecology is a very young field, and we can really only speculate what trauma P. aeruginosa went through as an evolutionary child to create this superhero. At any rate, this discovery is yet more evidence of how complex the microscopic world really is.

On a more practical level, by understanding what makes P. aeruginosa unsheath its T6SS, we might be able to re-establish a truce when this bacterium does cause infections. Eventually, we might even figure out how to hire it as a mercenary to supplement our own immune systems. I hear Basler et al. are working on a bat signal.

References
Basler, M., Ho, B.T.&Mekalanos, J.J., 2013. Tit-for-Tat: Type VI Secretion System Counterattack during Bacterial Cell-Cell Interactions. Cell, 152(4), pp.884–894.
By “accident” we mean, of course, a stochastic process following Poisson statistics.

Bio-Nanowires Conduct Electricity

ORIGINAL: Raijini Rao

▶ Imagine a conducting nanowire, only 3-5 nm wide but many thousand times longer, connecting a microbial community to form mini-power grids. Naturally occurring soil bacteria, such as Geobacter, use these conductivepili for long-range electron transport. How and why do they do this?

▶ All living organisms respire. Our cells break down sugars to obtain energy by extracting electrons that are handed down a relay chain to oxygen, which becomes water. The proteins (cytochromes) that conduct electrons are aided by special metallic centers, studded with iron, so they can cycle between Fe2+ (ferrous) and Fe3+ (ferric) states that differ by one electron. Geobacter uses these cytochromes too, just as our cells do. But oxygen only made its debut a mere 2.4 billion years ago. Before that, ancient bacteria shuttled the electrons to other acceptors, such as sulfides, nitrates and Fe3+. When Geobacter is deprived of oxygen, it grows out long pili into mineral rich rocks and "breathes" iron (drawing on top right). The current is believed to pass between layers of bacteria (middle right image) across a distance of 12 millimetres, which may not seem large, but is 10,000 body lengths to bacteria!

▶ But can proteins conduct current? Researchers knew that the pili were conductive, behaving like ohmic devices (image at bottom right). Although the pili were decorated with cytochromes, they were spaced too far apart to transfer electrons between their metallic centers. When the protein chains were mutated to replace a type of amino acid, the pili lost conductivity. These "aromatic" amino acids have pi-pi orbitals that may be conducting electrons.

▶ Live Wires: Bacterial nanowires can be used in generating microbial energy cells, bioremediation of pollutants (like uranium), and in nano-manufacturing of a variety of devices. The main image shows bacteria growing on metal electrodes.

⚛ Ref:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3604773/

⚛ Sources: http://www.geobacter.org/Nanowires,http://goo.gl/E6Kpf , http://goo.gl/si6aH ,http://goo.gl/T76L5

Microbes Thrive in Deepest Spot on Earth

ORIGINAL: Live Science

17 March 2013

The central part of the autonomous instrument that was deployed to measure the oxygen dynamics of the sea-bed in the Mariana Trench at a depth of 11 km. Data documented intensified microbial life in the bottom of the trench as compared to conditions at the surrounding abyssal plains at 6 km water depth.  CREDIT: Anni Glud 

The deepest oceanic trench on Earth is home to a surprisingly active community of bacteria, suggesting other trenches may be hotspots of microbial life, researchers say. 

Life in the deep ocean often relies on organic matter snowing down from above. As these particles waft down, their nutrients get degraded by microbes attached to them, so only 1 to 2 percent of the organic matter produced in surface waters is expected to make it to the average ocean depth of about 12,150 feet (3,700 meters). Just how much makes it to the very deepest parts is unknown. 

To learn more about life in the dirt at the ocean's depths, scientists used a submersible lander to analyze mud from the surface of Challenger Deep, the deepest spot of the Mariana Trench at the bottom of the central west Pacific Ocean. This 36,000-foot-deep (11,000 m) trench is the deepest known point on Earth's surface. 

Natural trap 

The researchers analyzed the levels of oxygen consumption within the sediments, which revealed how active the deep-sea microbes were. They discovered unexpectedly high rates of oxygen consumption from the Mariana seafloor, indicating a microbial community twice as active as that of a nearby 19,700-foot (6,000 m) site about 35 miles (60 kilometers) to the south. [Strangest Places Where Life Is Found on Earth] 

"In the most remote, inhospitable places, you can actually have higher activity than their surroundings," researcher Ronnie Glud, a biogeochemist at the Southern Danish University in Odense, Denmark, told OurAmazingPlanet. 

Sediments from Challenger Deep also had significantly higher levels of microbes and organic compounds than the nearby, more elevated site. The investigators suggest the Mariana Trench acts as a natural trap for sediments from up high. Similar effects are seen in other submarine canyons. 

"It acts as a trap just because it's a big hole. If you have a hole in a garden, it just fills up because things blowing over it tend to fall in, and the same is true with the seafloor," Glud said. The trench is also located in a subduction zone where one of the tectonic plates making up the surface of the Earth is diving under another, "and these areas are very unstable, and frequently see earthquakes that can trigger mudslides that transport material into the trench," he added. 

Microbes, microbes everywhere 

Another team of scientists recently discovered communities of microbes thriving in the oceanic crust. That research looked at rocks up to about 1,150 to 1,900 feet (350 to 580 m) below the seafloor under about 8,500 feet (2,600 m) of water off the coast of the northwestern United States. These microbes apparently live off energy from chemical reactions between water and rock instead of nutrients snowing from above. 

"You can find microbes everywhere — they're extremely adaptable to conditions, and survive wherever they are," Glud said. 

The researchers are now analyzing other trenches to see what bacterial activity is also relatively high there. They also want to learn more about the genetics of bacteria in the Mariana Trench and other trenches "to see how special these bacteria are compared to other bacteria," Glud said. 

The scientists detailed their findings online March 17 in the journal Nature Geoscience. 

Follow OurAmazingPlanet @OAPlanet, Facebook and Google+.

NASA Rover Finds Conditions Once Suited for Ancient Life on Mars

ORIGINAL: NASA

March 12, 2013

PASADENA, Calif. -- An analysis of a rock sample collected by NASA's Curiosity rover shows ancient Mars could have supported living microbes. 

Scientists identified sulfur, nitrogen, hydrogen, oxygen, phosphorus and carbon -- some of the key chemical ingredients for life -- in the powder Curiosity drilled out of a sedimentary rock near an ancient stream bed in Gale Crater on the Red Planet last month. 

"A fundamental question for this mission is whether Mars could have supported a habitable environment," said Michael Meyer, lead scientist for NASA's Mars Exploration Program at the agency's headquarters in Washington. "From what we know now, the answer is yes." 

Clues to this habitable environment come from data returned by the rover's Sample Analysis at Mars (SAM) and Chemistry and Mineralogy (CheMin) instruments. The data indicate the Yellowknife Bay area the rover is exploring was the end of an ancient river system or an intermittently wet lake bed that could have provided chemical energy and other favorable conditions for microbes. The rock is made up of a fine-grained mudstone containing clay minerals, sulfate minerals and other chemicals. This ancient wet environment, unlike some others on Mars, was not harshly oxidizing, acidic or extremely salty. 

The patch of bedrock where Curiosity drilled for its first sample lies in an ancient network of stream channels descending from the rim of Gale Crater. The bedrock also is fine-grained mudstone and shows evidence of multiple periods of wet conditions, including nodules and veins. 

Curiosity's drill collected the sample at a site just a few hundred yards away from where the rover earlier found an ancient streambed in September 2012. 

"Clay minerals make up at least 20 percent of the composition of this sample," said David Blake, principal investigator for the CheMin instrument at NASA's Ames Research Center in Moffett Field, Calif. 

These clay minerals are a product of the reaction of relatively fresh water with igneous minerals, such as olivine, also present in the sediment. The reaction could have taken place within the sedimentary deposit, during transport of the sediment, or in the source region of the sediment. The presence of calcium sulfate along with the clay suggests the soil is neutral or mildly alkaline. 

Scientists were surprised to find a mixture of oxidized, less-oxidized, and even non-oxidized chemicals, providing an energy gradient of the sort many microbes on Earth exploit to live. This partial oxidation was first hinted at when the drill cuttings were revealed to be gray rather than red. 

"The range of chemical ingredients we have identified in the sample is impressive, and it suggests pairings such as sulfates and sulfides that indicate a possible chemical energy source for micro-organisms," said Paul Mahaffy, principal investigator of the SAM suite of instruments at NASA's Goddard Space Flight Center in Greenbelt, Md. 

An additional drilled sample will be used to help confirm these results for several of the trace gases analyzed by the SAM instrument. 

"We have characterized a very ancient, but strangely new 'gray Mars' where conditions once were favorable for life," said John Grotzinger, Mars Science Laboratory project scientist at the California Institute of Technology in Pasadena, Calif. "Curiosity is on a mission of discovery and exploration, and as a team we feel there are many more exciting discoveries ahead of us in the months and years to come." 

Scientists plan to work with Curiosity in the "Yellowknife Bay" area for many more weeks before beginning a long drive to Gale Crater's central mound, Mount Sharp. Investigating the stack of layers exposed on Mount Sharp, where clay minerals and sulfate minerals have been identified from orbit, may add information about the duration and diversity of habitable conditions. 

NASA's Mars Science Laboratory Project has been using Curiosity to investigate whether an area within Mars' Gale Crater ever has offered an environment favorable for microbial life. Curiosity, carrying 10 science instruments, landed seven months ago to begin its two-year prime mission. NASA's Jet Propulsion Laboratory in Pasadena, Calif., manages the project for NASA's Science Mission Directorate in Washington. 

For more about the mission, visit: http://www.jpl.nasa.gov/msl , http://mars.jpl.nasa.gov/msl/ and http://www.nasa.gov/msl . You can follow the mission on Facebook and Twitter at: http://www.facebook.com/marscuriosity and http://www.twitter.com/marscuriosity

DC Agle 818-393-9011

Jet Propulsion Laboratory, Pasadena, Calif.

agle@jpl.nasa.gov 

Dwayne Brown 202-358-1726

NASA Headquarters, Washington

Dwayne.c.brown@nasa.gov

Two Different Aqueous Environments

This set of images compares rocks seen by NASA's Opportunity rover and Curiosity rover at two different parts of Mars. On the left is " Wopmay" rock, in Endurance Crater, Meridiani Planum, as studied by the Opportunity rover. 

First Curiosity Drilling Sample in the Scoop. This image from NASA's Curiosity rover shows the first sample of powdered rock extracted by the rover's drill. Image credit: NASA/JPL-Caltech/MSSS 

Minerals at 'Rocknest' and 'John Klein' 

This side-by-side comparison shows the X-ray diffraction patterns of two different samples collected from the Martian surface by NASA's Curiosity rover. These images, made from data obtained by Curiosity's Chemistry and Mineralogy instrument (CheMin), show the patterns obtained from a drift of windblown dust and sand called "Rocknest" and from a powdered rock sample drilled from the "John Klein" bedrock.

The presence of abundant clay minerals in the John Klein drill powder and the lack of abundant salt suggest a fresh water environment. The presence of calcium sulfates rather than magnesium or iron sulfates (as found at Meridiani Planum by NASA's Mars Exploration Rover Opportunity) suggests a neutral to mildly alkaline pH environment. The Rocknest sand shadow mineralogy suggests a dry, aeolian (wind-shaped) environment with low water activity. The John Klein mineralogy suggests a lacustrine (lakebed) environment with high water activity.

As seen on the left, the Rocknest data reveal abundant plagioclase feldspar, pyroxene and olivine minerals. The data also indicate reveal small amounts of magnetite and anhydrite. In addition, the Rocknest sample contains 25 to 35 percent amorphous, or non-crystalline, material.

X-ray diffraction analysis of the John Klein drill powder reveals abundant phyllosilicate (a class of clay minerals called smectites that form by the action of relatively pure and neutral pH water on source minerals), plagioclase feldspar, pyroxene, magnetite and olivine. Alternatively, the clay minerals could have been transported by water from sources higher up the sediment fan to form the John Klein mineral assemblage. The region of the pattern indicating the phyllosilicates is labeled in the annotated version of this image. The data also show minor amounts of anhydrite and bassanite. The John Klein sample also contains about 20 percent amorphous material.

NASA's Jet Propulsion Laboratory, a division of Caltech in Pasadena, manages the project for NASA's Science Mission Directorate, Washington, and built Curiosity and CheMin.

An Earth Analog to Mars' Yellowknife Bay. This set of images shows a modern terrestrial analog to the "Yellowknife Bay" area that NASA's Curiosity rover is exploring. At left is a sampling pit exposing clay-bearing lake sediments, deposited in a basaltic basin in southern Australia. Image Credit: NASA/JPL-Caltech/Ames 

Location of John Klein Drill Site 

Studying Habitability in Ancient Martian Environments

This set of images shows the results from the rock abrasion tool from NASA's Mars Exploration Rover Opportunity (left) and the drill from NASA's Curiosity rover (right). Note how the rock grindings from Opportunity are brownish red, indicating the presence of hematite, a strongly oxidized iron-bearing mineral. Such minerals are less supportive of habitability and also may degrade organic compounds. The diameter of the abraded circle is 1.8 inches (4.5 centimeters). The image was cropped from an image

 http://marsrover.nasa.gov/gallery/press/opportunity/20040305a/15-jb-02-hole2-B041R1.jpg, 

taken on Sol 35 (the 35th Martian day of Opportunity's operations, or Feb. 28, 2004, on Earth) by Opportunity's panoramic camera at a target called "Guadalupe" inside Eagle Crater.

On the right is the hole produced by Curiosity during the first drilling into a rock on Mars to collect a sample from inside the rock. In this case, the rock produced gray tailings -- not red -- suggesting the presence of iron that is less oxidized. One possibility is magnetite, which was determined to be present by Curiosity's Chemistry and Mineralogy instrument. Magnetite has less oxygen than hematite and would be more compatible with habitability and the preservation of organics, all other factors being equal. These other factors would include the primary concentration of organics in the sedimentary environment, in addition to later exposure of rock to surface radiation. The diameter of the hole is 0.63 inch (1.6 centimeters), which is approximately 1/3 of that on the left-hand image. The image was cropped fromPIA16726. It was taken on Sol 182 (the 182d Martian day of Curiosity's operations, or Feb. 8, 2013, on Earth) by the Mars Hand Lens Imager on Curiosity's arm after that day's drilling at a target rock called "John Klein."

JPL manages the Mars Science Laboratory/Curiosity for NASA's Science Mission Directorate in Washington. The rover was designed, developed and assembled at JPL, a division of the California Institute of Technology in Pasadena.

For more about NASA's Curiosity mission, visit: http://www.jpl.nasa.gov/msl, http://www.nasa.gov/mars, andhttp://mars.jpl.nasa.gov/msl.

Major Gases Released from Drilled Samples of the 'John Klein' Rock

An analysis of a drilled rock sample from NASA's Curiosity rover shows the presence of water, carbon dioxide, oxygen, sulfur dioxide, and hydrogen sulfide released on heating. The results analyzing the high temperature water release are consistent with smectite clay minerals.

Curiosity's Sample Analysis at Mars (SAM) instrument suite conducted the analysis. The first step in the analysis of a portion of this drilled sample was to heat the sample in a quartz oven to 1,535 degrees Farenheit (835 degrees Celsius) and analyze the gases as they were released using SAM's quadrupole mass spectrometer (QMS). The signatures of more than five hundred mass values were sampled during the heating of this drilled sample and analyzed by the QMS. Five are shown in the graph. These traces are diagnostic of water, carbon dioxide, oxygen, and two forms of sulfur (sulfur dioxide, the oxidized form, and hydrogen sulfide, the reduced form) measured by the QMS.

The second step in the analysis was to send a portion of the gas released from the sample to the tunable laser spectrometer (TLS) to measure isotopes of carbon, oxygen and hydrogen, in both water and carbon dioxide. The ratio of deuterium (a heavy form of hydrogen) to the lighter, more abundant form of hydrogen was lower than the deuterium-to-hydrogen ratio measured by SAM in more loosely bound water in the sample from the "Rocknest" drift. The high deuterium-to-hydrogen ratio in water in the Mars atmosphere is a signature of the lighter hydrogen more rapidly escaping to space over geological time. Therefore, measuring the deuterium-to-hydrogen in water released from rocks is one tool that can be used to explore ancient reservoirs of water on Mars.

The third step in the analysis was to inject gas trapped during the heating process into SAM's third instrument, the gas chromatograph. Individual compounds separate out in time in a long capillary column in this instrument and are then introduced into the QMS. The gas chromatograph mass spectrometer is a prime tool in the SAM search for organic compounds.

The ratio of reduced species to oxidized species released by the SAM ovens is significantly higher in this drilled bedrock than in the previously scooped dust samples. These results indicate a significant amount of available chemical energy because oxidized and less oxidized versions of molecules are present. This result, combined with suitable aqueous conditions at this site in the distant past, made this a potentially habitable environment.

The SAM analysis was conducted on Sol 200 (the 200th Martian day of Curosity's operations, which was Feb. 27, 2013, on Earth).

JPL manages the Mars Science Laboratory/Curiosity for NASA's Science Mission Directorate in Washington. The rover was designed, developed and assembled at JPL, a division of the California Institute of Technology in Pasadena.

For more about NASA's Curiosity mission, visit: http://www.jpl.nasa.gov/msl, http://www.nasa.gov/mars, andhttp://mars.jpl.nasa.gov/msl.

Chlorinated Forms of Methane at 'John Klein' Site

NASA's Curiosity rover has detected the simple carbon-containing compounds chloro- and dichloromethane from the powdered rock sample extracted from the "John Klein" rock on Mars. These species were detected by the gas chromatograph mass spectrometer (GCMS) on Curiosity's Sample Analysis at Mars instrument (SAM).

The blue peak on the left shows the presence of chloromethane and the two red peaks on the right show the presence of dichloromethane. The powdered rock sample from John Klein was heated and some of the gas released was injected into the capillary column of the GCMS. The time at which different compounds exited the gas chromatograph column and entered the mass spectrometer, and the patterns produced in the mass spectrometer indicated molecular identity.

This chart also indicates "blank runs," which were conducted on Mars prior to delivery of this drilled sample to SAM. The runs helped to insure that signals from the gases released from the John Klein sample were above background levels. Curiosity began drilling at John Klein in February 2013. The SAM analysis was conducted on Sol 200 (the 200th Martian day of Curosity's operations, which was Feb. 27, 2013, on Earth).

Both chloro- and dichloromethane were also detected earlier by SAM at the "Rocknest" drift. It is possible that these simple carbon-containing compounds were produced by the reaction between Martian carbon and chlorine released when this sample was heated in the SAM oven. However, analysis of an additional drilled sample is required to help scientists understand if instead any residual terrestrial carbon from the drill, or perhaps chlorine left over from the Rocknest sample, is responsible for the generation of some or all of these compounds. In any case, these detections demonstrate clearly that the SAM GCMS is performing as designed and ready to continue the search for organic compounds in Gale Crater.

JPL manages the Mars Science Laboratory/Curiosity for NASA's Science Mission Directorate in Washington. The rover was designed, developed and assembled at JPL, a division of the California Institute of Technology in Pasadena.

For more about NASA's Curiosity mission, visit: http://www.jpl.nasa.gov/msl, http://www.nasa.gov/mars, andhttp://mars.jpl.nasa.gov/msl.

Could the sea be conscious? Research reveals how tiny plankton behave like a marine 'megamind'

ORIGINAL: Daily Mail

By DAMIEN GAYLE

13 February 2013

U.S. researchers find that different forms of picoplankton react as one to environmental changes

Although as different as humans and fungi, the creatures' behaviour was linked

Findings could help researchers understand why some species are impossible to grow in isolation

Vastly different species of sea microbes work together to respond as one to their surroundings as if they have one 'megamind', new research has revealed.

U.S. researchers have discovered communities of infinitesimal creatures in our oceans react in unison to changes in their environment.

The links between them are not well understood, but findings suggest the creatures rely on each other to almost the same extent as the different cells in a human body.

Megamind: Despite the amazing diversity of marine microbes, a new research paper shows that many different groups work together to react in unison to their surroundings

As an example, if one set of the microbes were, say, creating energy through photosynthesis, which would then produce carbon dioxide, another set of microbes would somehow know and react - perhaps preparing to absorb the carbon dioxide.

The open sea contains an amazing diversity of extremely tiny organisms called picoplankton, which include relatively simple life forms such as marine bacteria, as well as more complicated organisms.

Microbiologists who study wild marine microbes, as opposed to the lab-grown variety, face enormous challenges in getting a clear picture of the daily activities of their subjects.

To take a look at these creatures in their natural habitat, researchers from the Massachusetts Institute of Technology and the Monterey Bay Aquarium Research Institute used a new method for collecting marine microbes.

They created a robotic sampling device which dangled beneath the waves to collect samples of one billion microbes every four hours.

Similar to fast photography that stops action, the robotic device 'fixed' each sample so that whatever genes the microbes were expressing at the moment of capture were preserved for later study.

After returning the samples to the lab, researchers used cutting-edge analysis techniques to figure out which genes within the microbes were actively being used at different times of day.

This involved sorting through millions of billions of fragments of genetic material and then assigning each fragment to a specific gene and a specific type of microbe.

In so doing they created a time-lapse montage of the daily labours of a range of microbial species over a two-day period.

A research vessel drifts near the buoy supporting the Environmental Sample Processor used to collect microbes for the experiment. Inset shows the yellow float with the ESP pressure housing suspended in the water

'A naturalist like Sir David Attenborough can follow a herd of elk and see how the elk’s behavior changes hour to hour, day to day and week to week,' said Edward DeLong, professor of environmental systems at MIT.

HOW RESEARCHERS 'FROZE TIME' TO MAKE THEIR FINDINGS

Using their robot microbe collecting device, researchers were able to gather samples of one billion microbes every four hours and keep them 'fixed' at the moment of collection.

This meant that whatever genes the microbes were expressing at the moment of capture were preserved for later study in the lab.

Microbes are extraordinarily sensitive to slight environmental changes, altering their gene expression rapidly in response to fluctuations in temperature, light, nutrient availability and other environmental variables.

Because of this, the genes they express tell a story about their habitat and their interactions with it.

In essence, changes in their gene expression provide information on the good times and the bad times they experience.

In a sense, each naturally occurring microbe is a living sensor and the researchers can read the sensors’ outputs by studying their gene expression.

By studying these environmental responses the MIT/MBARI team were able to make completely new findings about the behaviour of the creatures.

'But we haven’t been able to observe naturally occurring microbes with that kind of resolution until now.'

Professor DeLong, who is lead author of a paper in the Proceedings of the National Academy of Sciences detailing the research, added: 'We've essentially captured a day in the life of these microbes.

'As little as three years ago, I wouldn’t have even have considered it possible to get such a high resolution picture of microbial population dynamics and activity in the "real world".'

The montage showed photosynthetic microbes, which create the oxygen, energy and organic carbon used by the rest of the food web, ramped up their light-utilising activities in the morning and powered those down at night, just as their domestic brethren do in response to light and dark in the lab.

But the underwater scenes also showed something scientists had never seen before.

Non-photosynthetic, carbon-eating microbes of very different species displayed synchronised, rapidly varying metabolic gene expression - despite the fact that they came from groups as different as humans and fungi.

Some of the genes simultaneously expressed by different species shared the same function — for instance, genes associated with growth or respiration.

Others encoded very different functions, mirroring the varied metabolic capabilities of the disparate species.

'We've essentially captured a day in the life of these microbes': Researchers readying the robotic device connected to a buoy for its two-day sampling journey off the coast of California

The researchers hypothesised that all these microbes were reacting to the same environmental changes, but that different groups of microbes were responding in different ways.

Although the researchers cannot tell exactly which environmental changes the microbes were responding to, they suspect that the different groups of microbes were working together to obtain different types of food.

For example, some picoplankton could have been consuming large organic compounds such as proteins and fats. In the process, they could have produced simpler organic compounds, such as amino acids, which were then released into the surrounding seawater and consumed by other picoplankton.

'These results show a surprising amount of coordination between marine microbes,' said a spokesman for the Monterey Bay Aquarium Research Institute.

'They also suggest that, as in the food webs of larger organisms, many different groups of marine microbes rely on each other to survive on a day-to-day basis.

'This could help explain why so many species of marine microbes are difficult or impossible to grow by themselves in the lab.'

Bloom - Microbial Bebop

ORIGINAL: YouTube

This musical composition was created from data of microbes (bacteria, algae and other microorganisms) sampled in the English Channel. Argonne National Laboratory biologist Peter Larsen created the songs as a unique way to present and comprehend large datasets. 

This composition highlights seasonal patterns in marine physical parameters at the L4 Station. The chords are generated from seasonal changes in photosynthetically active radiation. The melody of each measure is comprised of eight notes, each mapped to a physical environmental parameter, in the following order: 

• temperature, 
• soluble reactive phosphate, 
• nitrate, 
• nitrite, 
• saline, 
• silicate and c
• hlorophyll A concentrations. 

More information at http://www.anl.gov/articles/songs-key-sea

Photo of cyanobacteria colonies is courtesy Specious Reasons

(http://www.flickr.com/photos/28594931@N03/4726914132/) at Flickr via 

Creative Commons.

"Esta generación encontrará vida extraterrestre"

ORIGINAL: La Vanguardia

21/08/2012 - 00:00

Victoria Meadows, astrobióloga y astrónoma planetaria. Foto: Llibert Teixidó

Directora feliz

La astrobiología es el estudio del origen, evolución, distribución y futuro de la vida en el universo, y esta doctora es la investigadora que dirige el Laboratorio Planetario Virtual de la NASA desde el 2000. Su misión es encontrar vida en la galaxia fuera de nuestro sistema solar y lo hace con buen humor y mucha energía: "Me pregunto por qué me pagan por hacerlo... ¡Es tan divertido!" Su acierto fue crear un grupo de científicos multidisciplinar y dinámico. Ha participado en el foro Cambridge Workshops on Cool Stars, Stellar Systems and the Sun. Nacido hace 30 años, reúne a los mayores expertos en estrellas frías, y este año lo ha organizado el Institut d'Estudis Espacials de Catalunya.

Cuándo fue la primera vez que se fijó en las estrellas?

Lo recuerdo muy bien porque yo tenía problemas de vista y a los once años mi madre me compró una gafas, miré hacia el cielo y me quedé maravillada.

Contágieme.

Yo dedico mi vida a estudiar los planetas que orbitan alrededor de las estrellas frías, en concreto las M, porque la posibilidad de que haya planetas habitables a su alrededor es muy alta.

Si no cualquier tipo de vida se asaría.

Exacto, si la estrella es muy caliente y el planeta está muy cerca, su agua se evapora, y el agua es esencial para la vida, y si está demasiado lejos, se congela. Las estrellas M son reactores nucleares muy pequeñitos.

¿Cómo buscan la vida?

A través de modelos teóricos que comprobamos con observaciones; estudiamos la interacción de la estrella y el planeta para ver cómo le afecta la radiación y la gravedad.

¿Hay muchos sistemas planetarios en nuestra galaxia?

Muchísimos, aunque con agua líquida sobre la superficie creemos que debe de haber poquísimos. Pero hay muchas lunas con agua en las que podemos encontrar vida bacteriana. El problema es que cuando lancemos el James Webb tendremos que elegir un solo candidato.

¿Cuántos planetas hay en la galaxia?

Sabemos de la existencia de 777 planetas extrasolares dentro de nuestra galaxia, de ellos un pequeño porcentaje son planetas rocosos como la Tierra, y ese es nuestro objetivo. Debe de haber muchísimos más, pero son muy pequeños y difíciles de detectar.

¿Y por qué tiene que ser rocoso?

Porque pueden albergar océanos sobre su superficie.

¿No sería posible que la vida en otros planeta no haya surgido del mar?

Para generar vida tiene que haber agua líquida, pero es una molécula muy común en el universo.

¿Y puede haber vida inteligente en esos planetas rocosos?

Creo que sí, pero lo que nosotros buscamos es vida microbiana, que es relativamente fáciles de ver a gran distancia porque sus efectos sobre el planeta son mucho más significativos que los de seres como nosotros.

Curioso.

Los microbios son pequeñitos, pero hay millones y millones de ellos. De hecho el oxígeno que respiramos viene de los microbios, que lo han ido produciendo a lo largo de dos mil millones de años. Y podemos observar ese oxígeno a grandes distancias. Se ve antes los efectos de los microbios que los de un elefante.

Da que pensar.

Los microbios pueden cambiar un ecosistema, incluso se ha estudiado la posibilidad de crear atmósfera en otro planeta.

Jugar a ser dioses.

El proyecto Terraforming pretende llevar microorganismos a Marte y crear las condiciones de evolución terrestres. Hay mucho interés, pero es tan a largo plazo que han optado por otras opciones por el momento.

¿Por ejemplo?

Llevar a la superficie el agua de Marte y traer muestras para estudiar la posible colonización del planeta.

¿Ha visto Avatar de James Cameron?

Sí, una luna rocosa habitada (lo que puede ser profético) por seres inteligentes (eso ya es más difícil) que viven en comunión con la naturaleza y que los humanos invaden para extraer minerales que, tal como nos comportamos, sería muy probable.

¿Paraísos verdes sin extraterrestres?

La fotosíntesis en planetas que tienen océanos se va a producir porque es una evolución natural, así que se generará toda la flora, sucederá y en abundancia.

Entonces, ¿cree que nosotros somos los más evolucionados?

La paradoja de Fermi dice que si existiese vida inteligente en otro sistema solar ya nos habrían encontrado, pero hay muchas soluciones a esta paradoja, como la ecuación de Drake's que demuestra la posibilidad de vida, así que a su pregunta mi respuesta es no lo sé.

¿Qué otras misiones hay en marcha en busca de vida en el universo?

La NASA tiene la misión Kepler, en órbita actualmente, que esta buscando la fracción de estrellas que puede albergar planetas en la zona de habitabilidad. El James Webb será lanzado en el 2018 o 2019 y el Terrestrial Planet Finder se lanzará en veinte años.

¿Qué ha descubierto sobre los seres humanos mirando las estrellas?

Cómo manejarlos, ja, ja. Controlar a mis científicos es como controlar un rebaño de gatos.

¿...?

No saben recibir órdenes. Hace millones de años mirábamos a las estrellas y nos preguntábamos si seríamos los únicos en el universo, esta generación tiene las capacidades tecnológicas para averiguarlo.

¿Cómo llega una mujer a ser una alta directiva de la NASA?

Presenté una propuesta sobre modelos teóricos para el observatorio planetario virtual y fuimos seleccionados, llevamos once años trabajando, ese laboratorio es mi criatura.

¿Qué les distingue?

La interdisciplinariedad, científicos de muy distinta calaña, desde biólogos moleculares hasta físicos estelares, trabajamos juntos.

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A New Energy Source: Major Advance Made in Generating Electricity from Wastewater

ORIGINAL: ScienceDaily

Hong Liu, an engineer at Oregon State University, has developed greatly improved new methods to produce electricity from the processing of wastewater. (Credit: Photo courtesy of Oregon State University)

ScienceDaily (Aug. 13, 2012) — Engineers at Oregon State University have made a breakthrough in the performance of microbial fuel cells that can produce electricity directly from wastewater, opening the door to a future in which waste treatment plants not only will power themselves, but will sell excess electricity.

The new technology developed at OSU can now produce 10 to 50 more times the electricity, per volume, than most other approaches using microbial fuel cells, and 100 times more electricity than some.

Researchers say this could eventually change the way that wastewater is treated all over the world, replacing the widely used "activated sludge" process that has been in use for almost a century. The new approach would produce significant amounts of electricity while effectively cleaning the wastewater.

The findings have just been published in Energy and Environmental Science, a professional journal, in work funded by the National Science Foundation.

"If this technology works on a commercial scale the way we believe it will, the treatment of wastewater could be a huge energy producer, not a huge energy cost," said Hong Liu, an associate professor in the OSU Department of Biological and Ecological Engineering. "This could have an impact around the world, save a great deal of money, provide better water treatment and promote energy sustainability."

Experts estimate that about 3 percent of the electrical energy consumed in the United States and other developed countries is used to treat wastewater, and a majority of that electricity is produced by fossil fuels that contribute to global warming.

Scientists use microbes to make 'clean' methane

ORIGINAL: Science Daily

ScienceDaily (July 27, 2012) — Microbes that convert electricity into methane gas could become an important source of renewable energy, according to scientists from Stanford and Pennsylvania State universities. 

Researchers at both campuses are raising colonies of microorganisms, called methanogens, which have the remarkable ability to turn electrical energy into pure methane -- the key ingredient in natural gas. The scientists' goal is to create large microbial factories that will transform clean electricity from solar, wind or nuclear power into renewable methane fuel and other valuable chemical compounds for industry.

"Most of today's methane is derived from natural gas, a fossil fuel," said Alfred Spormann, a professor of chemical engineering and of civil and environmental engineering at Stanford. "And many important organic molecules used in industry are made from petroleum. Our microbial approach would eliminate the need for using these fossil resources."

While methane itself is a formidable greenhouse gas, 20 times more potent than CO2, the microbial methane would be safely captured and stored, thus minimizing leakage into the atmosphere, Spormann said.

"The whole microbial process is carbon neutral," he explained. "All of the CO2 released during combustion is derived from the atmosphere, and all of the electrical energy comes from renewables or nuclear power, which are also CO2-free."

Methane-producing microbes, he added, could help solve one of the biggest challenges for large-scale renewable energy: What to do with surplus electricity generated by photovoltaic power stations and wind farms.

"Right now there is no good way to store electricity," Spormann said. "However, we know that some methanogens can produce methane directly from an electrical current. In other words, they metabolize electrical energy into chemical energy in the form of methane, which can be stored. Understanding how this metabolic process works is the focus of our research. If we can engineer methanogens to produce methane at scale, it will be a game changer."

'Green' methane

Burning natural gas accelerates global warming by releasing carbon dioxide that's been trapped underground for millennia. The Stanford and Penn State team is taking a "greener" approach to methane production. Instead of drilling rigs and pumps, the scientists envision large bioreactors filled with methanogens -- single-cell organisms that resemble bacteria but belong to a genetically distinct group of microbes called archaea.

By human standards, a methanogen's lifestyle is extreme. It cannot grow in the presence of oxygen. Instead, it regularly dines on atmospheric carbon dioxide and electrons borrowed from hydrogen gas. The byproduct of this microbial meal is pure methane, which methanogens excrete into the atmosphere.

The researchers plan to use this methane to fuel airplanes, ships and vehicles. In the ideal scenario, cultures of methanogens would be fed a constant supply of electrons generated from emissions-free power sources, such as solar cells, wind turbines and nuclear reactors. The microbes would use these clean electrons to metabolize carbon dioxide into methane, which can then be stockpiled and distributed via existing natural gas facilities and pipelines when needed.

When the microbial methane is burnt as fuel, carbon dioxide would be recycled back into the atmosphere where it originated from -- unlike conventional natural gas combustion, which contributes to global warming.

"Microbial methane is much more ecofriendly than ethanol and other biofuels," Spormann said. "Corn ethanol, for example, requires acres of cropland, as well as fertilizers, pesticides, irrigation and fermentation. Methanogens are much more efficient, because they metabolize methane in just a few quick steps."

Microbial communities

For this new technology to become commercially viable, a number of fundamental challenges must be addressed.

"While conceptually simple, there are significant hurdles to overcome before electricity-to-methane technology can be deployed at a large scale," said Bruce Logan, a professor of civil and environmental engineering at Penn State. "That's because the underlying science of how these organisms convert electrons into chemical energy is poorly understood."

In 2009, Logan's lab was the first to demonstrate that a methanogen strain known as Methanobacterium palustre could convert an electrical current directly into methane. For the experiment, Logan and his Penn State colleagues built a reverse battery with positive and negative electrodes placed in a beaker of nutrient-enriched water.

The researchers spread a biofilm mixture of M. palustre and other microbial species onto the cathode. When an electrical current was applied, the M. palustre began churning out methane gas.

"The microbes were about 80 percent efficient in converting electricity to methane," Logan said.

The rate of methane production remained high as long as the mixed microbial community was intact. But when a previously isolated strain of pure M. palustre was placed on the cathode alone, the rate plummeted, suggesting that methanogens separated from other microbial species are less efficient than those living in a natural community.

"Microbial communities are complex," Spormann added. "For example, oxygen-consuming bacteria can help stabilize the community by preventing the build-up of oxygen gas, which methanogens cannot tolerate. Other microbes compete with methanogens for electrons. We want to identify the composition of different communities and see how they evolve together over time."

Microbial zoo

To accomplish that goal, Spormann has been feeding electricity to laboratory cultures consisting of mixed strains of archaea and bacteria. This microbial zoo includes bacterial species that compete with methanogens for carbon dioxide, which the bacteria use to make acetate -- an important ingredient in vinegar, textiles and a variety of industrial chemicals.

"There might be organisms that are perfect for making acetate or methane but haven't been identified yet," Spormann said. "We need to tap into the unknown, novel organisms that are out there."

At Penn State, Logan's lab is designing and testing advanced cathode technologies that will encourage the growth of methanogens and maximize methane production. The Penn State team is also studying new materials for electrodes, including a carbon-mesh fabric that could eliminate the need for platinum and other precious metal catalysts.

"Many of these materials have only been studied in bacterial systems but not in communities with methanogens or other archaea," Logan said. "Our ultimate goal is to create a cost-effective system that reliably and robustly produces methane from clean electrical energy. It's high-risk, high-reward research, but new approaches are needed for energy storage and for making useful organic molecules without fossil fuels."

The Stanford-Penn State research effort is funded by a three-year grant from the Global Climate and Energy Project at Stanford.

Warming Will Unlock Carbon in Forests, Study Warns

ORIGINAL: NYTimes Green Blog

By FELICITY BARRINGER

Will Owens. Franceska Hopkins, the lead author of the study on the release of carbon from soil in forests.

Climate scientists have long been concerned about the possibility that warming temperatures will speed changes on the earth’s surface that will in turn accelerate global warming. The best illustration of such a feedback loop involves the melting of sea ice in the Arctic. The ice reflects solar radiation back into space rather than absorbing it. When it melts, it leaves open water that absorbs the heat rather than reflecting it. The more warm water there is, the more ice melts, and so on.

Now scientists have identified another feedback loop that may be accelerating the loss of carbon dioxide from the topsoil of forests in the United States, contributing to climate change. In a study published online on Monday, researchers at the University of California, Irvine and the Lawrence Berkeley National Laboratory found that the warmer it gets, the more active are the microbes that eat the topsoil and exhale carbon dioxide afterward.

While that finding is not surprising, said the lead author, Francesca Hopkins, a doctoral researcher in the Department of Earth System Science at Irvine, she and her collaborators also found that in warmer temperatures the microbes are better able to digest decades-old carbon stored in the soils. Scientists had previously that the old carbon was inaccessible because it had become fixed in the soil.

The study was published online in the Proceedings of the National Academy of Sciences.

“This has been really hotly debated in the past decade or so,” Ms. Hopkins said in an interview. “Some people think the older soil carbon would decompose more quickly” as temperatures increase, “and some think it wouldn’t decompose at all, because it had stabilized.” The mechanisms by which carbon is stabilized in the soil are poorly understood, although it is clear that some carbon molecules bind to mineral particles in the soil, she said.

But after collecting soils from woodlands in North Carolina and Wisconsin and putting them in mason jars, then storing the jars in incubators at different temperatures, “we saw that the microbes could access some carbon that is at least a decade old,” she said.

The age of the carbon was determined by the isotopes in the carbon dioxide exhaled by the microbes; carbon older than a decade has a distinctive isotope signature. The scientists were able to pinpoint the age of the carbon that had been stored for less than a decade more precisely by measuring a different set of isotopes.

The study reported an eightfold increase in carbon dioxide production when temperatures were increased by 20 degrees Celsius (36 degrees Fahrenheit). This is far in excess of the range of temperature increases predicted to occur by the end of the century under existing climate models. Under the moderate warming scenario predicted by the Intergovernmental Panel on Climate Change, Ms. Hopkins’s experiment indicated that the respiration rates of the microbes — and the amount of carbon-dioxide they exhale — would roughly double by 2100.

The ability to measure the age of the carbon in the soil could be an increasingly useful tool for scientists, although the measurements are still being refined. The components of soil, including decaying leaves, roots and other vegetable matter, store at least twice as much carbon as the chemicals in the atmosphere, according to United Nations climate reports.

The findings of the new study further complicate the dynamics underlying forests’ role in carbon storage. Forests are widely known as repositories of carbon — about 104 billion tons of it worldwide — but the role they will play in a warming world is less understood. If they become carbon emitters rather than carbon sinks as temperatures warm, projections of how fast climate change will occur may have to be adjusted.